These scripts allow to run the commandline version of Mykrobe Predictor in parallel for batches of sequence reads on macOSX.
batchMykrobe.sh will allow to run the command mykrobe predict staph on a set of samples with paired read files (fastq.gz). Using the -s flag, the results will be summarized in a table (requires adjusting the path to json_summary.py).
Summarizes the outputs from batchMykrobe.sh.
batchMykrobe.sh will allow to run the command mykrobe genotype on a set of samples with paired raw read files (fastq.gz). Using the -s flag, the results will be summarized in a table (requires adjusting the path to json_summary_genotype.py).
Summarizes the outputs from batchMykrobe_genotype.sh.
All scripts are tested on macOSX. Adjustments might be necessary for adapting them to linux. They depend on a working installation of the commandline version of Mykrobe Predictor with its dependencies. Bash scripts also depend on a working installation of GNU parallel